Dear Jari Oksanen,
Thanks a lot for the varpart R package help.
I preferred Adj. R square as mentioned by Peres-Neto (2006), but there
are two facts that let me struggling around with the adj. R square. a)
I received an Adj. R. square > 1 for an explanatory matrix (common and
individual fraction together; e.g. fraction a+d+f+g) and b) Adj. R.
square for "all fractions" is sometimes smaller than the individual
fraction. I used scale() for the explanatory variables, vif.cca and
forward selection in each explanatory matrix. I am therefore not sure
if this finding is really a statistical or data handling problem.
Additionally the dependend matrix consists of continuous tree
productivity variables. I would very much appreciate if you can give
me some hints if I have missed some specific R-varpart mathematical
functions explaining this finding.
Thanks a lot
Sibylle
On 23.08.2013, at 11:06, Jari Oksanen wrote:
Sibylle Stöckli <sibylle.stoeckli <at> gmx.ch> writes:
I applied vegan's varpart function to partition the effects of
explanatory matrices. Adj. R square for the unique fraction [a] is
0.25. Does anyone know why the decomposition by hand using rda gives
me a different result for [a] (constrained proportion is 0.32)? I
used
cbind() for the conditional fractions, but it should be similar to
condition()?
...
Df R.square Adj.R.square Testable
...
[a+b+d+e+f+g] = X1+X2 40 0.64676 0.49318 TRUE
[a+c+d+e+f+g] = X1+X3 38 0.59086 0.42546 TRUE
[b+c+d+e+f+g] = X2+X3 20 0.36936 0.25675 TRUE
[a+b+c+d+e+f+g] = All 49 0.69072 0.50813 TRUE
Individual fractions
[a] = X1 | X2+X3 29 0.25139 TRUE
...
Sibylle,
When you decompose by hand, you probably calculate
X1 | X2+X3 = All - X2+X3, or
0.32136 = 0.69072 - 0.36936,
whereas varpart function in vegan calculates this as
0.25139 = 0.50813 - 0.49318 (with smaller round-off error).
That is, vegan uses column "Adj.R.square", but you used column
"R.square"
in your hand calculation.
This is documented in ?varpart with a reference to publications where
this is justified (Peres-Neto et al. 2006, Legendre & Legendre 2012).
Sorry for excessive pruning of your original post: I use gmane to
post and it does not allow appropriate quoting of the original
message.
Cheers, Jari Oksanen
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